Ok guys, I have a situation where my boat is running a little warm (around 185-190). It's a 2001 Centurion Elite V with the black scorpion. The part to me that is perplexing is that the pump-side manifold is considerably warmer than is the one on the driver's side (starboard). The starboard side is nice and cool. I plan on replacing the impeller this weekend, but it seems odd to me that one side is cool while the other is warm to hot; particularly when the warmer side is actually closer to the water pump. One thought I had is that the heater could be cannibalizing some of the water from the pump-side? Would this make any sense?

I had a lot of issues with my boat regarding engine cooling and the heatrcraft heater . I have an aux heater pump because the length of water hose that was run and I found out they tied in the heater water hose to the wrong point. Is the heater a new install ? I would double check all of the tie points for the heater and verify they are in the appropriate points according to mercruiser/heatercraft recomendations.

You might want to run the boat on land with a Fake-a-Lake , or something on ti. Watch how much water is coming out of each exhaust. More water out one side should mean that side manifold is cooler.
Normally the heater return line is at the suction side of the circulation water pump. Normally the heater source line is on the intake manifold just before the thermostat. If the source line comes from close to one engine bank it may cause that side to be a bit cooler and that side manifold could be a bit cooler due to higher water flow on that side.
The flow out of the hotter manifold might be restricted. If it is restricted the system needs to be flushed.

This may be a dumb question, but how do you flush the system? I have a fitting that fits into the plug on the hose going off the water pump that is supposed to be for flushing after salt water usage. would that work?

So, I figured out that the motor is equipped with a fresh water flush. So , I hooked up the flush and ran the hose through the block for a while, and there was plenty of flow out of both sides. I then changed the impeller (the old one looked fine). I then hooked everything back up and started it up. Boat seemed to be running nice and cool. Then, after about 20 min, it heated up a bit. Not too terrible, but around 185.. I'm wondering if I could have a clog somewhere.